Experience was with B5 Passats 99 to 06?
There was a SoCal VW dealer who was very mod friendly if the mods were purchased through him and installed by him (IMHO his prices were competitive). To my knowledge he never invalidated a warranty repair if it was related to anything installed by him. Passat owners from all over CA. flocked to him for engine mods, improved chips (engine and tranny), suspension mods etc. It sounded good and was, EXCEPT, other dealers didn't accept his warranty -duh. So you drive from Fresno to LA, you have your car tarted up and modded at this dealer. All,s good? Then a few weeks later you have an issue, your cars won't run and you're in Fresno. The local dealer says, " your aftermarket chip or whatever caused this failure. We'll fix it but it's on your dime". Now you have two choices, pay up or tow the car to SoCal. More than one owner faced this issue.
I'm just saying that if you mod your car, even thru a mod friendly dealer, you may need to be prepared to deal with your non mod friendly dealers (ie pay up) and have a Plan B if a major failure occurs that that local dealer will not repair under warranty.
One of my friends had an engine failure while on a road trip to Oregon. He ended up paying a small fortune to have it trailered back to SoCal (less however than the cost of an engine rebuild in Eugene). Also had rental car expense to get back home.
IMHO-If you want to keep your warranty clean. Don't mod your car, anywhere